NAME

Bio::Search::Tiling::MapTiling - An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics

SYNOPSIS

# get a BLAST $hit from somewhere, then
$tiling = Bio::Search::Tiling::MapTiling->new($hit);

# stats
$numID = $tiling->identities();
$numCons = $tiling->conserved();
$query_length = $tiling->length('query');
$subject_length = $tiling->length('subject'); # or...
$subject_length = $tiling->length('hit');

# get a visual on the coverage map
print $tiling->coverage_map_as_text('query',$context,'LEGEND');

# tilings
$context = $tiling->_context( -type => 'subject', -strand=> 1, -frame=>1);
@covering_hsps_for_subject = $tiling->next_tiling('subject',$context);
$context = $tiling->_context( -type => 'query', -strand=> -1, -frame=>0);
@covering_hsps_for_query   = $tiling->next_tiling('query', $context);

DESCRIPTION

Frequently, users want to use a set of high-scoring pairs (HSPs) obtained from a BLAST or other search to assess the overall level of identity, conservation, or coverage represented by matches between a subject and a query sequence. Because a set of HSPs frequently describes multiple overlapping sequence fragments, a simple summation of statistics over the HSPs will generally overestimate those statistics. To obtain an accurate estimate of global hit statistics, a 'tiling' of HSPs onto either the subject or the query sequence must be performed, in order to properly correct for this.

This module will execute a tiling algorithm on a given hit based on an interval decomposition I'm calling the "coverage map". Internal object methods compute the various statistics, which are then stored in appropriately-named public object attributes. See Bio::Search::Tiling::MapTileUtils for more info on the algorithm.

STRAND/FRAME CONTEXTS

In BLASTX, TBLASTN, and TBLASTX reports, strand and frame information are reported for the query, subject, or query and subject, respectively, for each HSP. Tilings for these sequence types are only meaningful when they include HSPs in the same strand and frame, or "context". So, in these situations, the context must be specified in the method calls or the methods will throw.

Contexts are specified as strings: [ 'all' | [m|p][_|0|1|2] ], where all = all HSPs (will throw if context must be specified), m = minus strand, p = plus strand, and _ = no frame info, 0,1,2 = respective (absolute) frame. The "_make_context_key" method will convert a (strand, frame) specification to a context string, e.g.:

$context = $self->_context(-type=>'query', -strand=>-1, -frame=>-2);

returns m2.

The contexts present among the HSPs in a hit are identified and stored for convenience upon object construction. These are accessed off the object with the "contexts" method. If contexts don't apply for the given report, this returns ('all').

TILED ALIGNMENTS

The experimental method "get_tiled_alns" in ALIGNMENTS will use a tiling to concatenate tiled hsps into a series of Bio::SimpleAlign objects:

@alns = $tiling->get_tiled_alns($type, $context);

Each alignment contains two sequences with ids 'query' and 'subject', and consists of a concatenation of tiling HSPs which overlap or are directly adjacent. The alignment are returned in $type sequence order. When HSPs overlap, the alignment sequence is taken from the HSP which comes first in the coverage map array.

The sequences in each alignment contain features (even though they are Bio::LocatableSeq objects) which map the original query/subject coordinates to the new alignment sequence coordinates. You can determine the original BLAST fragments this way:

$aln = ($tiling->get_tiled_alns)[0];
$qseq = $aln->get_seq_by_id('query');
$hseq = $aln->get_seq_by_id('subject');
foreach my $feat ($qseq->get_SeqFeatures) {
   $org_start = ($feat->get_tag_values('query_start'))[0];
   $org_end = ($feat->get_tag_values('query_end'))[0];
   # original fragment as represented in the tiled alignment:
   $org_fragment = $feat->seq;
}
foreach my $feat ($hseq->get_SeqFeatures) {
   $org_start = ($feat->get_tag_values('subject_start'))[0];
   $org_end = ($feat->get_tag_values('subject_end'))[0];
   # original fragment as represented in the tiled alignment:
   $org_fragment = $feat->seq;
}

DESIGN NOTE

The major calculations are made just-in-time, and then memoized. So, for example, for a given MapTiling object, a coverage map would usually be calculated only once (for the query), and at most twice (if the subject perspective is also desired), and then only when a statistic is first accessed. Afterward, the map and/or any statistic is read from storage. So feel free to call the statistic methods frequently if it suits you.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

CONSTRUCTOR

new

Title   : new
Usage   : my $obj = new Bio::Search::Tiling::GenericTiling();
Function: Builds a new Bio::Search::Tiling::GenericTiling object 
Returns : an instance of Bio::Search::Tiling::GenericTiling
Args    : -hit    => $a_Bio_Search_Hit_HitI_object
          general filter function:
          -hsp_filter => sub { my $this_hsp = shift; 
                               ...;
                               return 1 if $wanted;
                               return 0; }

TILING ITERATORS

next_tiling

Title   : next_tiling
Usage   : @hsps = $self->next_tiling($type);
Function: Obtain a tiling: a minimal set of HSPs covering the $type
          ('hit', 'subject', 'query') sequence
Example :
Returns : an array of HSPI objects
Args    : scalar $type: one of 'hit', 'subject', 'query', with
          'subject' an alias for 'hit'

rewind_tilings

Title   : rewind_tilings
Usage   : $self->rewind_tilings($type)
Function: Reset the next_tilings($type) iterator
Example :
Returns : True on success
Args    : scalar $type: one of 'hit', 'subject', 'query';
          default is 'query'

ALIGNMENTS

get_tiled_alns()

Title   : get_tiled_alns
Usage   : @alns = $tiling->get_tiled_alns($type, $context)
Function: Use a tiling to construct a minimal set of alignment 
          objects covering the region specified by $type/$context
          by splicing adjacent HSP tiles
Returns : an array of Bio::SimpleAlign objects; see Note below
Args    : scalar $type: one of 'hit', 'subject', 'query'
          default is 'query'
          scalar $context: strand/frame context string
          Following $type and $context, an array of 
          ordered, tiled HSP objects can be specified; this is 
          the tiling that will directly the alignment construction
          default -- the first tiling provided by a tiling iterator
Notes   : Each returned alignment is a concatenation of adjacent tiles.
          The set of alignments will cover all regions described by the 
          $type/$context pair in the hit. The pair of sequences in each 
          alignment have ids 'query' and 'subject', and each sequence 
          possesses SeqFeatures that map the original query or subject 
          coordinates to the sequence coordinates in the tiled alignment.

STATISTICS

identities

Title   : identities
Usage   : $tiling->identities($type, $action, $context)
Function: Retrieve the calculated number of identities for the invocant
Example : 
Returns : value of identities (a scalar)
Args    : scalar $type: one of 'hit', 'subject', 'query'
          default is 'query'
          option scalar $action: one of 'exact', 'est', 'fast', 'max'
          default is 'exact'
          option scalar $context: strand/frame context string
Note    : getter only

conserved

Title   : conserved
Usage   : $tiling->conserved($type, $action)
Function: Retrieve the calculated number of conserved sites for the invocant
Example : 
Returns : value of conserved (a scalar)
Args    : scalar $type: one of 'hit', 'subject', 'query'
          default is 'query'
          option scalar $action: one of 'exact', 'est', 'fast', 'max'
          default is 'exact'
          option scalar $context: strand/frame context string
Note    : getter only

length

Title   : length
Usage   : $tiling->length($type, $action, $context)
Function: Retrieve the total length of aligned residues for 
          the seq $type
Example : 
Returns : value of length (a scalar)
Args    : scalar $type: one of 'hit', 'subject', 'query'
          default is 'query'
          option scalar $action: one of 'exact', 'est', 'fast', 'max'
          default is 'exact'
          option scalar $context: strand/frame context string
Note    : getter only

frac

Title   : frac
Usage   : $tiling->frac($type, $denom, $action, $context, $method)
Function: Return the fraction of sequence length consisting
          of desired kinds of pairs (given by $method), 
          with respect to $denom
Returns : scalar float
Args    : -type => one of 'hit', 'subject', 'query'
          -denom => one of 'total', 'aligned'
          -action => one of 'exact', 'est', 'fast', 'max'
          -context => strand/frame context string
          -method => one of 'identical', 'conserved'
Note    : $denom == 'aligned', return desired_stat/num_aligned
          $denom == 'total', return desired_stat/_reported_length
            (i.e., length of the original input sequences)
Note    : In keeping with the spirit of Bio::Search::HSP::HSPI, 
          reported lengths of translated dna are reduced by 
          a factor of 3, to provide fractions relative to 
          amino acid coordinates.

frac_identical

Title   : frac_identical
Usage   : $tiling->frac_identical($type, $denom, $action, $context)
Function: Return the fraction of sequence length consisting
          of identical pairs, with respect to $denom
Returns : scalar float
Args    : -type => one of 'hit', 'subject', 'query'
          -denom => one of 'total', 'aligned'
          -action => one of 'exact', 'est', 'fast', 'max'
          -context => strand/frame context string
Note    : $denom == 'aligned', return conserved/num_aligned
          $denom == 'total', return conserved/_reported_length
            (i.e., length of the original input sequences)
Note    : In keeping with the spirit of Bio::Search::HSP::HSPI, 
          reported lengths of translated dna are reduced by 
          a factor of 3, to provide fractions relative to 
          amino acid coordinates. 
Note    : This an alias that calls frac()

frac_conserved

Title   : frac_conserved
Usage   : $tiling->frac_conserved($type, $denom, $action, $context)
Function: Return the fraction of sequence length consisting
          of conserved pairs, with respect to $denom
Returns : scalar float
Args    : -type => one of 'hit', 'subject', 'query'
          -denom => one of 'total', 'aligned'
          -action => one of 'exact', 'est', 'fast', 'max'
          -context => strand/frame context string
Note    : $denom == 'aligned', return conserved/num_aligned
          $denom == 'total', return conserved/_reported_length
            (i.e., length of the original input sequences)
Note    : In keeping with the spirit of Bio::Search::HSP::HSPI, 
          reported lengths of translated dna are reduced by 
          a factor of 3, to provide fractions relative to 
          amino acid coordinates. 
Note    : This an alias that calls frac()

frac_aligned

Title   : frac_aligned
Aliases : frac_aligned_query - frac_aligned(-type=>'query',...)
          frac_aligned_hit   - frac_aligned(-type=>'hit',...)
Usage   : $tiling->frac_aligned(-type=>$type,
                                -action=>$action,
                                -context=>$context)
Function: Return the fraction of input sequence length
          that was aligned by the algorithm
Returns : scalar float
Args    : -type => one of 'hit', 'subject', 'query'
          -action => one of 'exact', 'est', 'fast', 'max'
          -context => strand/frame context string

num_aligned

Title   : num_aligned
Usage   : $tiling->num_aligned(-type=>$type)
Function: Return the number of residues of sequence $type
          that were aligned by the algorithm
Returns : scalar int
Args    : -type => one of 'hit', 'subject', 'query'
          -action => one of 'exact', 'est', 'fast', 'max'
          -context => strand/frame context string
Note    : Since this is calculated from reported coordinates,
          not symbol string counts, it is already in terms of
          "logical length"
Note    : Aliases length()

num_unaligned

Title   : num_unaligned
Usage   : $tiling->num_unaligned(-type=>$type)
Function: Return the number of residues of sequence $type
          that were left unaligned by the algorithm
Returns : scalar int
Args    : -type => one of 'hit', 'subject', 'query'
          -action => one of 'exact', 'est', 'fast', 'max'
          -context => strand/frame context string
Note    : Since this is calculated from reported coordinates,
          not symbol string counts, it is already in terms of
          "logical length"

range

Title   : range
Usage   : $tiling->range(-type=>$type)
Function: Returns the extent of the longest tiling
          as ($min_coord, $max_coord)
Returns : array of two scalar integers
Args    : -type => one of 'hit', 'subject', 'query'
          -context => strand/frame context string

ACCESSORS

coverage_map

Title   : coverage_map
Usage   : $map = $tiling->coverage_map($type)
Function: Property to contain the coverage map calculated
          by _calc_coverage_map() - see that for 
          details
Example : 
Returns : value of coverage_map_$type as an array
Args    : scalar $type: one of 'hit', 'subject', 'query'
          default is 'query'
Note    : getter

coverage_map_as_text

Title   : coverage_map_as_text
Usage   : $tiling->coverage_map_as_text($type, $legend_flag)
Function: Format a text-graphic representation of the
          coverage map
Returns : an array of scalar strings, suitable for printing
Args    : $type: one of 'query', 'hit', 'subject'
          $context: strand/frame context string
          $legend_flag: boolean; add a legend indicating
           the actual interval coordinates for each component
           interval and hsp (in the $type sequence context)
Example : print $tiling->coverage_map_as_text('query',1);

hit

Title   : hit
Usage   : $tiling->hit
Function: 
Example : 
Returns : The HitI object associated with the invocant
Args    : none
Note    : getter only

hsps

Title   : hsps
Usage   : $tiling->hsps()
Function: Container for the HSP objects associated with invocant
Example : 
Returns : an array of hsps associated with the hit
Args    : on set, new value (an arrayref or undef, optional)

contexts

Title   : contexts
Usage   : @contexts = $tiling->context($type) or
          @indices = $tiling->context($type, $context)
Function: Retrieve the set of available contexts in the hit,
          or the indices of hsps having the given context
          (integer indices for the array returned by $self->hsps)
Returns : array of scalar context strings or 
          array of scalar positive integers
          undef if no hsps in given context
Args    : $type: one of 'query', 'hit', 'subject'
          optional $context: context string

mapping

Title   : mapping
Usage   : $tiling->mapping($type)
Function: Retrieve the mapping coefficient for the sequence type
          based on the underlying algorithm
Returns : scalar integer (mapping coefficient)
Args    : $type: one of 'query', 'hit', 'subject'
Note    : getter only (set in constructor)

default_context

Title   : default_context
Usage   : $tiling->default_context($type)
Function: Retrieve the default strand/frame context string
          for the sequence type based on the underlying algorithm
Returns : scalar string (context string)
Args    : $type: one of 'query', 'hit', 'subject'
Note    : getter only (set in constructor)

algorithm

Title   : algorithm
Usage   : $tiling->algorithm
Function: Retrieve the algorithm name associated with the 
          invocant's hit object
Returns : scalar string 
Args    : none
Note    : getter only (set in constructor)

"PRIVATE" METHODS

Calculators

See Bio::Search::Tiling::MapTileUtils for lower level calculation methods.

_calc_coverage_map

Title   : _calc_coverage_map
Usage   : $tiling->_calc_coverage_map($type)
Function: Calculates the coverage map for the object's associated
          hit from the perspective of the desired $type (see Args:) 
          and sets the coverage_map() property
Returns : True on success
Args    : optional scalar $type: one of 'hit'|'subject'|'query'
          default is 'query'
Note    : The "coverage map" is an array with the following format:
          ( [ $component_interval => [ @containing_hsps ] ], ... ),
          where $component_interval is a closed interval (see 
          DESCRIPTION) of the form [$a0, $a1] with $a0 <= $a1, and
          @containing_hsps is an array of all HspI objects in the hit 
          which completely contain the $component_interval.
          The set of $component_interval's is a disjoint decomposition
          of the minimum set of minimal intervals that completely
          cover the hit's HSPs (from the perspective of the $type)
Note    : This calculates the map for all strand/frame contexts available
          in the hit

_calc_stats

Title   : _calc_stats
Usage   : $tiling->_calc_stats($type, $action, $context)
Function: Calculates [estimated] tiling statistics (identities, conserved sites
          length) and sets the public accessors
Returns : True on success
Args    : scalar $type: one of 'hit', 'subject', 'query'
          default is 'query'
          optional scalar $action: requests calculation method
           currently one of 'exact', 'est', 'fast', 'max'
          option scalar $context: strand/frame context string
Note    : Action: The statistics are calculated by summing quantities
          over the disjoint component intervals, taking into account
          coverage of those intervals by multiple HSPs. The action
          tells the algorithm how to obtain those quantities--
          'exact' will use Bio::Search::HSP::HSPI::matches
           to count the appropriate segment of the homology string;
          'est' will estimate the statistics by multiplying the 
           fraction of the HSP overlapped by the component interval
           (see MapTileUtils) by the BLAST-reported identities/postives
           (this may be convenient for BLAST summary report formats)
          * Both exact and est take the average over the number of HSPs
            that overlap the component interval.
          'max' uses the exact method to calculate the statistics, 
           and returns only the maximum identites/positives over 
           overlapping HSP for the component interval. No averaging
           is involved here.
          'fast' doesn't involve tiling at all (hence the name),
           but it seems like a very good estimate, and uses only
           reported values, and so does not require sequence data. It
           calculates an average of reported identities, conserved
           sites, and lengths, over unmodified hsps in the hit,
           weighted by the length of the hsps.

Tiling Helper Methods

_make_tiling_iterator

Title   : _make_tiling_iterator
Usage   : $self->_make_tiling_iterator($type)
Function: Create an iterator code ref that will step through all 
          minimal combinations of HSPs that produce complete coverage
          of the $type ('hit', 'subject', 'query') sequence, 
          and set the correct iterator property of the invocant
Example :
Returns : The iterator
Args    : scalar $type, one of 'hit', 'subject', 'query';
          default is 'query'

_tiling_iterator

Title   : _tiling_iterator
Usage   : $tiling->_tiling_iterator($type,$context)
Function: Retrieve the tiling iterator coderef for the requested 
          $type ('hit', 'subject', 'query')
Example : 
Returns : coderef to the desired iterator
Args    : scalar $type, one of 'hit', 'subject', 'query'
          default is 'query'
          option scalar $context: strand/frame context string
Note    : getter only

Construction Helper Methods

_make_context_key

Title   : _make_context_key
Alias   : _context
Usage   : $tiling->_make_context_key(-strand => $strand, -frame => $frame)
Function: create a string indicating strand/frame context; serves as 
          component of memoizing hash keys
Returns : scalar string
Args    : -type => one of ('query', 'hit', 'subject')
          -strand => one of (1,0,-1)
          -frame  => one of (-2, 1, 0, 1, -2)
          called w/o args: returns 'all'

_context

Title   : _context
Alias   : _make_context_key
Usage   : $tiling->_make_context_key(-strand => $strand, -frame => $frame)
Function: create a string indicating strand/frame context; serves as 
          component of memoizing hash keys
Returns : scalar string
Args    : -type => one of ('query', 'hit', 'subject')
          -strand => one of (1,0,-1)
          -frame  => one of (-2, 1, 0, 1, -2)
          called w/o args: returns 'all'

Predicates

Most based on a reading of the algorithm name with a configuration lookup.

_has_sequence_data()
_has_logical_length()
_has_strand()
_has_frame()

Private Accessors

_contig_intersection

Title   : _contig_intersection
Usage   : $tiling->_contig_intersection($type)
Function: Return the minimal set of $type coordinate intervals
          covered by the invocant's HSPs
Returns : array of intervals (2-member arrayrefs; see MapTileUtils)
Args    : scalar $type: one of 'query', 'hit', 'subject'

_reported_length

Title   : _reported_length
Usage   : $tiling->_reported_length($type)
Function: Get the total length of the seq $type
          for the invocant's hit object, as reported
          by (not calculated from) the input data file
Returns : scalar int
Args    : scalar $type: one of 'query', 'hit', 'subject'
Note    : This is kludgy; the hit object does not currently
          maintain accessors for these values, but the 
          hsps possess these attributes. This is a wrapper
          that allows a consistent access method in the 
          MapTiling code.
Note    : Since this number is based on a reported length,
          it is already a "logical length".

To install BioPerl, copy and paste the appropriate command in to your terminal.

cpanm

cpanm BioPerl

CPAN shell

perl -MCPAN -e shell
install BioPerl

For more information on module installation, please visit the detailed CPAN module installation guide.

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